Agrobacterium rhizogenes or Rhizobium rhizogenes is able to transform plant genomes and induce the production of "hairy roots". We describe the use of A. rhizogenes in tomato to rapidly assess gene expression and function. Gene expression is indistinguishable in plants transformed by A. tumefaciens as compared to A. rhizogenes. A root cell-type and tissue-specific promoter resource has been generated for domesticated and wild tomato (Solanum lycopersicum and S. pennellii) using these approaches. Imaging of tomato roots using A. rhizogenes coupled with laser scanning confocal microscopy is facilitated by the use of a TagRFP marker present in binary vectors. Tomato-optimized Isolation of Nuclei Tagged in specific Cell-Types (INTACT) and Translating Ribosome Affinity Purification (TRAP) binary vectors were generated and used to monitor associated mRNA abundance or chromatin modification. Finally, transcriptional reporters, translational reporters and CRISPR/Cas9 genome editing demonstrate that SHORT-ROOT and SCARECROW gene function is conserved between Arabidopsis and tomato.